How to add the ancestral allele (AA) information in a vcf file?

Question

[taniamahmood38]

Dear all,

I have a VCF file from which I want to compute site frequency spectrum (sfs) statistics using rehh package on R. There I came to know that rehh accepts polarized vcf file meaning the file which has ancestral allele information in it (the AA tag), but my vcf doesn't has this info. Kindly tell me the tool and command to add the AA tag in vcf file. Any help would be highly appreciated

Thanks in advance

Answer 1

[Pierre Lindenbaum]

I wrote http://lindenb.github.io/jvarkit/VcfAncestralAllele.html for a colleague.

$ java -jar dist/vcfancestralalleles.jar \
    -m /commun/data/pubdb/ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/human_ancestor_GRCh37_e59/manifest.mf \
    src/test/resources/gnomad.exomes.r2.0.1.sites.vcf.gz |\
    bcftools annotate -x '^INFO/AA'

(...)
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
1   905606  rs540662886 G   C,A 41743.9 PASS    AA=G
1   905608  rs770396126 G   T,A 1006.45 PASS    AA=G
1   905609  .   G   A   694.04  PASS    AA=G
1   905610  rs775689041 TG  AG,T,TGGGGGGCCCAG   4327.1  PASS    AA=TG
1   905611  rs749351425 G   T   2434.35 PASS    AA=G
1   905616  .   G   C   1801.88 PASS    AA=G
1   905617  rs376988925 C   T,G 4379.6  PASS    AA=C
1   905619  rs774441222 C   T   19350.2 PASS    AA=C

[taniamahmood38]

Thanks for the help. But kindly clarify that if the vcfancestralallele command will work on any specie vcf file other than human?

Thanks

[Pierre Lindenbaum]

no, unless you have file similar to http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/

[taniamahmood38]

Okay but I dont have this file so is there any other way to do that? Kindly let me know, thank you